It doesn't logically follow that the only case where the 1000 year reference applies is in the context of God's mercy. The comment is a poetic illustration of the Eternity of God. The phrase could as easily have been a billion years.
A day, 1000 years, or 1,000,000,000 years... all are infinitesmal motes to God.
'If you think that is true, then find me another reference where a 1000 years = one day. The reference of time when God is speaking either is an absurd number, like the billion you mention, or it is a number Humans can grasp and understand. God uses the long time period of 1000 years being equal to a day because it is a metaphor used to speak of God's willingness to wait for us to repent.
This passage has NOTHING to do with Creation at all!! Those who use it to defend some long term age or whatever are misusing the verse. It is clear that this reference to 1000 years is about God's mercy, not the creation of the world in any sense at all.